High resolution array analysis: Diagnosing pregnancies with abnormal ultrasound findings

Journal of Medical Genetics

Volumn 46, Issue 8, 2009, Pages 531-541

  Tyreman, M ^a   Abbott, K M ^a   Willatt, L R ^a   Nash, R ^a   Lees, C ^a   Whittaker, J ^a   Simonic, I ^a  

^a ADDENBROOKE S HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA;

ALLELE; ARTICLE; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CHROMOSOME HIGH RESOLUTION BANDING ANALYSIS; CONGENITAL MALFORMATION; DIAGNOSTIC TEST; DNA EXTRACTION; EARLY DIAGNOSIS; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LOCATION; GENETIC VARIABILITY; GENOME; GENOME ANALYSIS; GENOTYPE; HETEROZYGOSITY; HETEROZYGOSITY LOSS; HUMAN; HUMAN CELL; HUMAN TISSUE; KARYOTYPE; LEARNING DISORDER; MAJOR CLINICAL STUDY; POLYMERASE CHAIN REACTION; PREGNANCY; PRENATAL SCREENING; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME ABERRATIONS; COHORT STUDIES; CONGENITAL ABNORMALITIES; FEMALE; GENE DELETION; GENE DOSAGE; GENE EXPRESSION; GENOME, HUMAN; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLOIDIES; POLYMORPHISM, SINGLE NUCLEOTIDE; PREGNANCY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; ULTRASONOGRAPHY, PRENATAL;

EID: 68049117211     PISSN: 00222593     EISSN: 14686244     Source Type: Journal    
DOI: 10.1136/jmg.2008.065482     Document Type: Article

References (46)

1. Benn PA, Egan JF, Fang M, Smith-Bindman R. Changes in the utilization of prenatal diagnosis. Obstet Gynecol 2004;103:1255-60
2. Caine A, Maltby AE, Parkin CA, Waters JJ, Crolla JA, UK Association of Clinical Cytogeneticists (ACC). Prenatal detection of Down's syndrome by rapid aneuploidy testing for chromosomes 13, 18, and 21 by FISH or PCR without a full karyotype: a cytogenetic risk assessment. Lancet 2005;366:123-8.
3. Shaw-Smith C, Pittman AM, Willatt L, Martin H, Rickman L, Gribble S, Curley R, Cumming S, Dunn C, Kalaitzopoulos D, Porter K, Prigmore E, Krepischi-Santos AC, Varela MC, Koiffmann CP, Lees AJ, Rosenberg C, Firth HV, de Silva R, Carter NP. Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability. Nat Genet 2006;38:1032-7.
4. Koolen DA, Vissers LE, Pfundt R, de Leeuw N, Knight SJ, Regan R, Kooy RF, Reyniers E, Romano C, Fichera M, Schinzel A, Baumer A, Anderlid BM, Schoumans J, Knoers NV, van Kessel AG, Sistermans EA, Veltman JA, Brunner HG, de Vries BB. A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat Genet 2006;38:999-1001.
5. Koolen DA, Sharp AJ, Hurst JA, Firth HV, Knight SJ, Goldenberg A, Saugier-Veber P, Pfundt R, Vissers LE, Destrée A, Grisart B, Rooms L, Van der Aa N, Field M, Hackett A, Bell K, Nowaczyk MJ, Mancini GM, Poddighe PJ, Schwartz CE, Rossi E, De Gregori M, Antonacci-Fulton LL, McLellan MD 2nd, Garrett JM, Wiechert MA, Miner TL, Crosby S, Ciccone R, Willatt L, Rauch A, Zenker M, Aradhya S, Manning MA, Strom TM, Wagenstaller J, Krepischi-Santos AC, Vianna-Morgante AM, Rosenberg C, Price SM, Stewart H, Shaw-Smith C, Brunner HG, Wilkie AO, Veltman JA, Zuffardi O, Eichler EE, de Vries BB. Clinical and molecular delineation of the 17q21.31 microdeletion syndrome. J Med Genet 2008;45:710-20.
6. Ben-Shachar S, Ou Z, Shaw CA, Belmont JW, Patel MS, Hummel M, Amato S, Tartaglia N, Berg J, Sutton VR, Lalani SR, Chinault AC, Cheung SW, Lupski JR, Patel A. 22q11.2 distal deletion: a recurrent genomic disorder distinct from DiGeorge syndrome and velocardiofacial syndrome. Am J Hum Genet 2008;82:214-21.
7. Ballif BC, Hornor SA, Jenkins E, Madan-Khetarpal S, Surti U, Jackson KE, Asamoah A, Brock PL, Gowans GC, Conway RL, Graham JM Jr, Medne L, Zackai EH, Shaikh TH, Geoghegan J, Selzer RR, Eis PS, Bejjani BA, Shaffer LG. Discovery of a previously unrecognized microdeletion syndrome of 16p11.2-p12.2. Nat Genet 2007;39:1071-3.
8. Rajcan-Separovic E, Harvard C, Liu X, McGillivray B, Hall JG, Qiao Y, Hurlburt J, Hildebrand J, Mickelson EC, Holden JJ, Lewis ME. Clinical and molecular cytogenetic characterisation of a newly recognised microdeletion syndrome involving 2p15-16.1. J Med Genet 2007;44:269-76.
9. McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, Altshuler DM, International HapMap Consortium. Common deletion polymorphisms in the human genome. Nat Genet 2006;38:86-92.
10. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE. Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 2005;77:78-88.
11. de Smith AJ, Tsalenko A, Sampas N, Scheffer A, Yamada NA, Tsang P, Ben-Dor A, Yakhini Z, Ellis RJ, Bruhn L, Laderman S, Froguel P, Blakemore AI. Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases. Hum Mol Genet 2007;16:2783-94.
12. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007;17:1665-74.
13. Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 2007;39:S48-54.
14. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 2008;40:1166-74.
15. WTCCC. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007;447:661-78.
16. Rauch A, Zink S, Zweier C, Thiel CT, Koch A, Rauch R, Lascorz J, Hüffmeier U, Weyand M, Singer H, Hofbeck M. Systematic assessment of atypical deletions reveals genotype-phenotype correlation in 22q11.2. J Med Genet 2005;42:871-6.
17. Kurahashi H, Nakayama T, Osugi Y, Tsuda E, Masuno M, Imaizumi K, Kamiya T, Sano T, Okada S, Nishisho I. Deletion mapping of 22q11 in CATCH22 syndrome: identification of a second critical region. Am J Hum Genet 1996;58:1377-81.
18. Garcia-Miñaur S, Fantes J, Murray RS, Porteous ME, Strain L, Burns JE, Stephen J, Warner JP. A novel atypical 22q11.2 distal deletion in father and son. J Med Genet 2002;39:e62.
19. Xu J, Fun YS, Siu VM. A child with features of Goldenhar syndrome and a novel 1.12 Mb deletion in 22q11.2 by cytogenetics and oligonucleotide array CGH: is this a candidate region for the syndrome? Am J Med Genet A 2008;146A:1886-9.
20. Klaassens M, Galjaard RJ, Scott DA, Brüggenwirth HT, van Opstal D, Fox MV, Higgins RR, Cohen-Overbeek TE, Schoonderwaldt EM, Lee B, Tibboel D, de Klein A. Prenatal detection and outcome of congenital diaphragmatic hernia (CDH) associated with deletion of chromosome 15q26: two patients and review of the literature. Am J Med Genet A 2007;143A:2204-12.
21. Lurie IW. Kidney abnormalities in persons with monosomy 15q26. Am J Med Genet A 2008;146A:1761-4.
22. Pereira FA, Qiu Y, Zhou G, Tsai M-J, Tsai SY. The orphan nuclear receptor COUP-TFII is required for angiogenesis and heart development. Genes Dev 1999;13:1037-49.
23. Pober BR. Genetic aspects of human congenital diaphragmatic hernia. Clin Genet 2008;74:1-15.
24. Holden ST, Cox JJ, Kesterton I, Thomas NS, Carr C, Woods CG. Fanconi anaemia complementation group B presenting as X linked VACTERL with hydrocephalus syndrome. J Med Genet 2006;43:750-4.
25. Cotter PD, McCurdy LD, Gershin IF, Babu A, Willner JP, Desnick RJ. Prenatal detection and molecular characterization of a de novo duplication of the distal long arm of chromosome 19. Am J Med Genet 1997;71:325- 8.
26. Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, Collins A, Mercer C, Norga K, de Ravel T, Devriendt K, Bongers EM, de Leeuw N, Reardon W, Gimelli S, Bena F, Hennekam RC, Male A, Gaunt L, Clayton-Smith J, Simonic I, Park SM, Mehta SG, Nik-Zainal S, Woods CG, Firth HV, Parkin G, Fichera M, Reitano S, Giudice ML, Li KE, Casuga I, Broomer A, Conrad B, Schwerzmann M, Räber L, Gallati S, Striano P, Coppola A, Tolmie JL, Tobias ES, Lilley C, Armengol L, Spysschaert Y, Verloo P, De Coene A, Goossens L, Mortier G, Speleman F, van Binsbergen E, Nelen MR, Hochstenbach R, Poot M, Gallagher L, Gill M, McClellan J, King MC, Regan R, Skinner C, Stevenson RE, Antonarakis SE, Chen C, Estivill X, Menten B, Gimelli G, Gribble S, Schwartz S, Sutcliffe JS, Walsh T, Knight SJ, Sebat J, Romano C, Schwartz CE, Veltman JA, de Vries BB, Vermeesch JR, Barber JC, Willatt L, Tassabehji M, Eichler EE. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med 2008;359:1685-99.
27. Brunetti-Pierri N, Berg JS, Scaglia F, Belmont J, Bacino CA, Sahoo T, Lalani SR, Graham B, Lee B, Shinawi M, Shen J, Kang SH, Pursley A, Lotze T, Kennedy G, Lansky-Shafer S, Weaver C, Roeder ER, Grebe TA, Arnold GL, Hutchison T, Reimschisel T, Amato S, Geragthy MT, Innis JW, Obersztyn E, Nowakowska B, Rosengren SS, Bader PI, Grange DK, Naqvi S, Garnica AD, Bernes SM, Fong CT, Summers A, Walters WD, Lupski JR, Stankiewicz P, Cheung SW, Patel A. Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities. Nat Genet 2008;40:1466-71.
28. Sonek J. First trimester ultrasonography in screening and detection of fetal anomalies. Am J Med Genet 2007;145C:45-61.
29. Knight MA, Kennerson ML, Anney RJ, Matsuura T, Nicholson GA, Salimi-Tari P, Gardner RJM, Storey E, Forrest SM. Spinocerebellar ataxia type 15 (SCA15) maps to 3p24.2-3pter: exclusion of the ITPR1 gene, the human orthologue of an ataxic mouse mutant. Neurobiol Dis 2003;13:147-57.
30. Iwaki A, Kawano Y, Miura S, Shibata H, Matsuse D, Li W, Furuya H, Ohyagi Y, Taniwaki T, Kira J, Fukumaki Y. Heterozygous deletion of ITPR1, but not SUMF1, in spinocerebellar ataxia type 16. J Med Genet 2008;45:32-5.
31. Barber JC. Terminal 3p deletions: phenotypic variability, chromosomal non-penetrance, or gene modification? Am J Med Genet A 2008;146A:1899-901.
32. Malmgren H, Sahlén S, Wide K, Lundvall M, Blennow E. Distal 3p deletion syndrome: detailed molecular cytogenetic and clinical characterisation of three small distal deletions and review. Am J Med Genet A 2007;146A:2143-9.
33. Griggs BL, Ladd S, Saul RA, DuPont BR, Srivastava AK. Dedicator of cytokinesis 8 is disrupted in two patients with mental retardation and developmental disabilities. Genomics 2008;91:195-202.
34. Lerer I, Sagi M, Meiner V, Cohen T, Zlotogora J, Abeliovich D. Deletion of the ANKRD15 gene at 9p24.3 causes parent-of-origin-dependent inheritance of familial cerebral palsy. Hum Mol Genet 2005;14:3911-20.
35. Farrell SA, Sue-Chue-Lam A, Miskin M, Yao-Shan Fan. Fetal nuchal oedema and antenatal diagnosis of trisomy 10. Prenatal Diagnosis 1994;14:463-7.
36. Woods CG, Cox J, Springell K, Hampshire DJ, Mohamed MD, McKibbin M, Stern R, Raymond LR, Sandford R, Malik-Sharif S, Karbani G, Ahmed M, Bond J, Clayton D, Inglehearn CF. Quantifications of homozygosity in consanguineous individuals with autosomal recessive disease. Am J Hum Genet 2006;78:889-96.
37. Shaffer LG, Coppinger J, Alliman S, Torchia BA, Theisen A, Ballif BC, Bejjani BA. Comparison of microarray-based detection rates for cytogenetic abnormalities in prenatal and neonatal specimens. Prenat Diagn 2008;28:789-95.
38. Le Caignec C, Boceno M, Saugier-Veber P, Jacquemont S, Joubert M, David A, Frebourg T, Rival JM. Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J Med Genet 2005;42:121-8.
39. Stankiewicz P, Beaudet AL. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr Opin Genet Dev 2007;17:182-92.
40. Manning M, Hudgins L. Use of array-based technology in the practice of medical genetics. Genet Med 2007;9:650-3.
41. Zahir F, Friedman JM. The impact of array genomic hybridization on mental retardation research: a review of current technologies and their clinical utility. Clin Genet 2007;72:271-87.
42. Palomares Bralo M, Delicado A, Lapunzina P, Valázquez R, Villa O, Ángeles Mori M, de Torres ML, Fernández L, Pérez Jurado LA, López Pajares I. Direct tandem duplication in chromosome 19q characterized by array CGH. Eur J Med Genet 2008;51:257-63.
43. Bruno DL, Ganesamoorthy D, Schoumans J, Bankier A, Coman D, Delatycki M, Gardner MR, Hunter M, James PA, Kannu P, McGillivray G, Pachter N, Peters H, Rieubland C, Savarirayan R, Scheffer IE, Sheffield L, Tan T, White SM, Yeung A, Bowman Z, Ngo C, Choy K, Cacheux V, Wong L, Amor D, Slater HR. Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice. J Med Genet 2009;46:123-31.
44. Rosenberg C, Knijnenburg J, Bakker E, Vianna-Morgante AM, Sloos W, Otto PA, Kriek M, Hansson K, Krepischi-Santos AC, Fiegler H, Carter NP, Bijlsma EK, van Haeringen A, Szuhai K, Tanke HJ. Array-CGH detection of micro rearrangements in mentally retarded individuals: clinical significance of imbalances present both in affected children and normal parents. J Med Genet 2006;43:180-6.
45. de Ravel TJ, Balikova I, Thienpont B, Hannes F, Maas N, Fryns JP, Devriendt K, Vermeesch JR. Molecular karyotyping of patients with MCA/MR: the blurred boundary between normal and pathogenic variation. Cytogenet Genome Res 2006;115:225-30.
46. Bisgaard AM, Kirchhoff M, Nielsen JE, Brandt C, Hove H, Jepsen B, Jensen T, Ullmann R, Skovby F. Transmitted cytogenetic abnormalities in patients with mental retardation: pathogenic or normal variants? Eur J Med Genet 2007;50:243-55.